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Dichter
BIAC Faculty
190 Posts |
 Posted - Nov 04 2006 : 1:07:45 PM
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I was trying to save my FSL model specifications and could not proceed because of some sort of memory issues. Here the error message I received. Any suggestions? Thank you.
error writing "file9": no space left on device
error writing "file9": no space left on device
while executing
"puts $channel "
# FEAT version number
set fmri(version) $fmri(version)
# Analysis level
# 1 : First-level analysis
# 2 : Higher-level analysis
set fm..."
(procedure "feat5:write" line 19)
invoked from within
"feat5:write $w 1 0 0 $fmri(feat_filename) "
(procedure "feat5:setup_model_preview" line 6)
invoked from within
"feat5:setup_model_preview .r"
invoked from within
".wdialog1.btns.b.view invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .wdialog1.btns.b.view"
(command bound to event) |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 05 2006 : 09:29:55 AM
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"No space left on device" typically means disk, not memory.
There have been lots of people using FSL recently on golgi, and it uses the /tmp directory for several of its temporary files. Unfortunately FSL doesn't clean up after itself very well if it doesn't complete. I have set up a nightly job to remove files in /tmp that are more than 7 days old, but sometimes this is not enough, and I have been manually removing files younger than that in the past couple weeks.
Alternatively, it may also be possible that you have hit your experiment quota, though I don't know if it is true in your case.
I will see if there is a better solution to this. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Nov 06 2006 : 10:01:36 AM
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There's an option when running at least the first-level analyses:
# Cleanup first-level standard-space images
set fmri(sscleanup_yn)
Would it help the memory problems if we select this option?
Dharol |
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petty
BIAC Staff
USA
453 Posts |
Posted - Nov 06 2006 : 10:03:16 AM
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| yes it will help conserve space further down the road. |
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Dichter
BIAC Faculty
190 Posts |
Posted - Nov 06 2006 : 10:56:05 AM
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Thanks a lot, Syam. No this is a new study, so it was not exceeding an experiment quota.
FYI, we were also unable to run bputil on Friday because of memory problems. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 06 2006 : 11:07:28 AM
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quote:
Originally posted by Dichter
Thanks a lot, Syam. No this is a new study, so it was not exceeding an experiment quota.
FYI, we were also unable to run bputil on Friday because of memory problems.
Memory problems? Or disk problems? I don't think bputil should encounter memory problems unless your runs have a large number of timepoints. |
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Dichter
BIAC Faculty
190 Posts |
Posted - Nov 06 2006 : 11:08:19 AM
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| Sorry - disk problems. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Nov 16 2006 : 1:10:01 PM
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I have been trying to run 3rd level FEAT analysis on Reward.01 data for over a week and always get the message
no space left on disk
I have deleted some files and continue to get this message. Is there an alternative place to GOLGI to run these analyses or some other fix?
Dharol |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 16 2006 : 1:57:54 PM
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Dharol,
This is due to /tmp filling up, not your data directories.
I have installed a new version of FSL that now respects the TMPDIR variable but have not yet made it easy to get TMPDIR set. I will post again soon how to get this working. In the meantime I have removed some files from /tmp. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Nov 29 2006 : 2:54:20 PM
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I'm a bit unclear on the latest updates to FSL and their implications, but am still having memory problems.
I cleaned out my users/tmp directory and am only running 3 FSL jobs, but am still geting the
Unable to open design.mat
Error: FILM did not complete - it probably ran out of memory
/mnt/katz/data/ExecInfo.09/Data/FSL/31385/run5
Error: FILM did not complete - it probably ran out of memory
Is there some new thing I'm not doing, or should we stick to running 1 job at a time?
Also, is there an easy way to pick up analysis wherever it stalled instead of starting over?
Thanks,
Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 29 2006 : 3:45:10 PM
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Does the FILM error happen consistently for certain analyses, or does it run successfully if you keep re-running it? Disk space should not be a problem anymore since /data/users has a lot of space. It's also hard to imagine that you are running out of memory, but perhaps that's what's happening -- does your data have a large number of timepoints?
I'm not aware of any way to restart FSL in the middle.
The report is complaining about not finding design.mat. Does that file exist in the .feat directories in which you see this error? Perhaps that's why FILM is exiting with an error... |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Nov 30 2006 : 12:31:30 PM
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The FILM error has been happening reliably lately. About two weeks ago it started consistently crashing at this place and giving me this error; before that, it was completing a good percentage of the time (I think then it really was probably memory problems).
FEAT is supposed to create
design.mat, design.con, design.frf, design.fsf, design.gif, design.ppm, and design.trg
Now when it's crashing and gives me this error message, it has only created design.con and design.fsf.
I took a look at the design.fsf for a run that completed and one that did not, and there do not appear to be any differences; the log report doesn't have any extra info either . . .?
Thanks,
Dharol |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Dec 01 2006 : 12:44:00 PM
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FYI, the error
Unable to open design.mat
Error: FILM did not complete - it probably ran out of memory
was due to some of the 3 column format files having commas that they weren't supposed to have.
Dharol
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vinod
Average Member
USA
68 Posts |
Posted - Jun 11 2007 : 07:20:49 AM
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quote:
I'm not aware of any way to restart FSL in the middle.
Given that FSL is basically executing instructions one by one at command line and saving all these commands to report.log file, is it possible to just save a smaller subset of these commands and run them as a shell script? This would mean restarting FSL in the middle? Let me know if this would work? |
Vinod Venkatraman
IPCN Graduate Student
Huettel Lab
"UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity." - Dennis Ritchie |
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petty
BIAC Staff
USA
453 Posts |
Posted - Jun 11 2007 : 08:57:06 AM
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| yes, if you pull out the lines that you are interested in from a log file, you should be able to directly run those from the command line. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jun 11 2007 : 09:04:03 AM
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Hi Vinod.
Logically what you say is sound; What i have not been able to figure out is which output files from crashed analysis to input into the new command line when starting in the middle.
If your analysis got through basic preprocessing steps (i.e., if you ended up with the file filtered_func_data.nii.gz, it's pretty easy to start the analysis from this point.
Instructions here http://fourier.biac.duke.edu/wiki/doku.php/huettel:rerunning_fsl |
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Topic |
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FSL memory problems?
